Settings

The Global Settings button on the home page, next to Import Workflow, opens the settings for all of N-WAVE. In its execution settings, a workflow can choose another run profile and lower limits of its own, but never higher limits than the global ones.

Notifications

N-WAVE can send browser notifications while you're in another tab or window:

• a run finished (with how long it took),
• a run failed or was stopped (with the reason, as the run panel explains it),
• N-WAVE can't be reached any more, and again when it's back.

Turn on Send browser notifications; the browser asks for permission then (not before). Choose which events to be told about, and use Send test notification to check that they show up. If nothing shows up, check your system's notification settings (Focus, Do Not Disturb). Clicking a run's notification opens its workflow with the run panel.

Notifications only come while the N-WAVE tab isn't in view; when it is, the page shows the same itself. With several N-WAVE tabs open, each event is notified once. The choices are kept in this browser.

Browsers allow notifications only for pages on HTTPS or on this computer (localhost). When N-WAVE is opened over plain HTTP from another machine, the page says so; open it at http://localhost or put it behind HTTPS. If the browser blocks N-WAVE's notifications, allow them in the site settings (the icon left of the address) and reload the page.

Run limits

Maximum CPU Cores, Maximum Memory and Execution Timeout: the most any run may use. Workflows use these unless they set lower ones (Execution Settings → Resources, with Use the global limits turned off). A workflow's limits above these are lowered to them, and its settings say so. The page shows what the server allows: higher values are lowered to NWAVE_MAX_CPUS and NWAVE_MAX_MEMORY, and a timeout of 0 uses NWAVE_EXECUTION_TIMEOUT (24 hours unless set). Each step may run as long as the run.

Resume

When Resume starts out on by the Run button: after a failed or stopped run (the default), whenever earlier runs left a cache, or never. The switch can always be changed before a run.

Run profiles

The run profiles and the one runs use (Runs use by default). Workflows follow it, also when it changes later, unless Execution Settings → Profiles → Use the global run profile is turned off and they choose another profile or this computer. Workflows from before Global Settings keep running on this computer until you choose otherwise.

Click Save global settings to apply changes. The run limits, Resume, profiles and feature switches are kept by N-WAVE (in settings.json in its data folder), so every browser uses the same.

Run cache

How much space the run cache of all workflows takes, and Clear all caches. Folders of runs that are still going are left alone. Results, inputs and logs stay. A single workflow's cache is in its execution settings.

Features

Switch N-WAVE's features on and off, for example to keep a course or a lab's installation simple, or to compare how people work with and without a feature. Off hides a feature; it doesn't break anything: workflows that use it still open and run. The switches apply to everyone using this N-WAVE and are saved as soon as you change one (no Save needed).

Switch	Name for NWAVE_FEATURES	Off
Workflow check before running	workflowCheck	block (the default): problems keep Run disabled. warn: they're shown, but the workflow can run. off: no check (Nextflow reports the problems when the run fails).
Connection hints	connectionHints	Inputs don't light up while dragging a connection, and connections that don't fit get no warning.
Minimap	minimap	No minimap of the whole workflow at the bottom left of the canvas.
Failure explanations	failureExplanations	A failed run shows its log, without an explanation in plain language.
Glossary and Help	glossary	No ⓘ term explanations, and no Help button or page.
Templates and built-in examples	templates	New Workflow starts an empty workflow, and the built-in demos and the tutorial are hidden. Their links still open.
Custom code	customCode	No custom processes, Code tab or converting nodes to custom ones. Workflows with custom code still run.
Node packs	nodePacks	Node packs can't be added, exported or managed. Nodes from installed packs still work.
Resume	resume	Every run starts from scratch; the Resume switch and the run cache settings are hidden.
Run profiles	runProfiles	Runs use this computer; run profiles can't be chosen or edited.
Notifications	notifications	No browser notifications, and their settings are hidden.
Run performance and reports	performance	No Performance tab, execution report or timeline after a run.
Workflow analysis	analysis	No Analyse button: the workflow's code isn't checked with nextflow lint and BioFlow-Insight, and its structure isn't shown (Workflow analysis).
When steps run	conditions	Steps show no conditions from the analysis, and aren't greyed out by the parameters' values (When a step runs).

Verbose mode is switched the same way (verbose, off by default) and can be fixed by the installation too.

Every run records which features were on when it started (in the run history, runs.json in N-WAVE's data folder), so runs can be compared later.

Fixing switches for an installation

Whoever runs N-WAVE can fix switches when it starts, so they can't be changed in the app. A fixed switch shows Fixed by this installation and can't be clicked. Set either or both:

• NWAVE_FEATURES: a comma-separated list, e.g. NWAVE_FEATURES="connectionHints=off,workflowCheck=warn". On/off switches take on or off (also true/false, yes/no, 1/0); workflowCheck takes block, warn or off.
• NWAVE_FEATURES_FILE: the path of a JSON file, e.g. {"connectionHints": false, "workflowCheck": "warn"}.

Where both name the same switch, NWAVE_FEATURES wins. Names or values N-WAVE doesn't know are skipped, with a warning in the backend's log. Switches that neither sets can still be changed in the app.

Verbose mode

Verbose mode records what happens in N-WAVE, to debug problems people report and for short usability tests. It is off by default. Turn it on under Verbose mode → Record what happens, or fix it for an installation with NWAVE_FEATURES="verbose=on" (see above). While it records, a marker at the top of every page says Recording.

What is recorded

One event per line (JSON), each with an id, its time (ISO 8601), its type, the browser tab's session, the participant ID and marked test if set, the open workflowId, the page (path) and the event's data:

Type	When	data
session.started	Recording begins in a browser tab	features: the switches in effect; recordsValues
features.changed	A feature switch changed	features
ui.click	A button, link, tab or menu entry was clicked	element, name (its label)
workflow.opened	A workflow was opened	nodes, edges (counts)
node.added, node.removed	A node was added or removed (also by paste, undo or a template)	nodeId, nodeType, label
node.moved	Nodes were moved (once the drag ends)	nodeIds
node.configured	A node's settings changed (once typing pauses)	nodeId, nodeType, label, keys: the settings changed
connection.made, connection.removed	A connection was made or removed	edgeId, source, sourceHandle, target, targetHandle; hint when the ports don't fit
connection.rejected	A connection was dropped on an input that refused it	the same, and the reason shown
check.result	The workflow check's result changed	mode, problems (id, level)
run.started	A run started	resume, and the workflow's nodes and connections (a snapshot)
run.ended	A run finished, failed or was stopped	runId, outcome, durationMs, reason
run.results	A finished run's results were read	runId, steps (name, status, durationMs), files (result paths)
failure.explained	A failure explanation was shown	kind, title, certainty, process
failure.feedback	Did this help? was answered under a failure explanation	kind, certainty, helpful (true or false)
analysis.run	The workflow was analysed (Analyse)	lint, bioflow (each done, unavailable or failed), errors, warnings; or failed
analysis.structureViewed	The analysis's structure view was switched	view (steps or channels)
analysis.downloaded	The analysed structure was downloaded	format (mermaid or dot), view
conditions.preview	The steps that won't run with the parameter values changed (after an analysis, or a value's change)	notRunning (node IDs), conditional (steps with a condition)
canvas.viewChanged	The canvas view was switched (Editor, Process graph, Groups)	view (all, steps or grouped)
group.created	Steps were grouped into a subworkflow	steps (how many), from (selection or suggestion)
group.renamed	A group was renamed	–
group.removed	A group was ungrouped	steps (how many it had)
nested.opened	The steps inside a subworkflow or pipeline node were opened	nodeId (from the canvas) or step (from inside), depth
help.opened, glossary.opened, code.opened	Help, a glossary explanation (term) or a node's Code tab (nodeId) was opened
undo, redo	Undo or redo
workflow.imported, workflow.exported	A workflow was imported (format: nextflow or daw-model) or exported (kind: script, script-copy, project, daw-model or diagram, with its source and format)
test.started, test.ended	A marked test began or ended	label

Not recorded: names, what is typed into fields, file contents and parameter values. An installation can record parameter values and file contents too with NWAVE_VERBOSE_VALUES=on (for debugging; the Settings page says when it does); then node.configured has the new values and the run snapshots have each node's settings.

Participant ID and marked tests

Participant ID sets a pseudonymous code for this browser, e.g. P07 (letters, digits, - and _ only, never a name); every event from the browser carries it. For a short test with a participant, click Start test in the marker at the top (with an optional label) and End test when done: the events in between carry the test's id and can be exported on their own.

Export, bug reports and clearing

• Download ZIP exports everything, the events between two dates, or one marked test: events.jsonl (the events), events.csv (the same as a table, with data as JSON), snapshots/ (the workflow at each run; run.started names its file) and a README.
• Copy for bug report copies the last 10 minutes as text to paste into a GitHub issue.
• Keep events for drops older events after 7, 30 or 90 days or a year; Clear log… deletes them all.

The events are kept by N-WAVE in activity.jsonl in its data folder, for the whole installation; in the browser demo, in this browser's local storage. While verbose mode is off, nothing is kept.